Persistent homology is a common technique in topological data analysis providing geometrical and topological information about the sample space. All this information, known as topological features, is summarized in persistence diagrams, and the main interest is in identifying the most persisting ones since they correspond to the Betti number values. Given the randomness inherent in the sampling process, and the complex structure of the space where persistence diagrams take values, estimation of Betti numbers is not straightforward. The approach followed in this work makes use of features’ lifetimes and provides a full Bayesian clustering model, based on random partitions, in order to estimate Betti numbers. A simulation study is also presented.

Change point analyses are concerned with identifying positions of an ordered stochastic process that undergo abrupt local changes of some underlying distribution. When multiple processes are observed, it is often the case that information regarding the change point positions is shared across the different processes. This work describes a method that takes advantage of this type of information. Since the number and position of change points can be described through a partition with contiguous clusters, our approach develops a joint model for these types of partitions. We describe computational strategies associated with our approach and illustrate improved performance in detecting change points through a small simulation study. We then apply our method to a financial data set of emerging markets in Latin America and highlight interesting insights discovered due to the correlation between change point locations among these economies.

We consider Bayesian nonparametric inference for event time distributions based on current status data. We show that under dependent censoring conventional mixture priors, including the popular Dirichlet process mixture prior, lead to biologically uninterpretable results as they unnaturally skew the probability mass for the event times toward the extremes of the observed data. Simple assumptions on dependent censoring can fix the problem. We then extend the discussion to bivariate current status data with partial ordering of the two outcomes. In addition to dependent censoring, we also exploit some minimal known structure relating the two event times. We design a Markov chain Monte Carlo algorithm for posterior simulation. Applied to a recurrent infection study, the method provides novel insights into how symptoms-related hospital visits are affected by covariates.

In various applications, we deal with high-dimensional positive-valued data that often exhibits sparsity. This paper develops a new class of continuous global-local shrinkage priors tailored to analyzing gamma-distributed observations where most of the underlying means are concentrated around a certain value. Unlike existing shrinkage priors, our new prior is a shape-scale mixture of inverse-gamma distributions, which has a desirable interpretation of the form of posterior mean and admits flexible shrinkage. We show that the proposed prior has two desirable theoretical properties; Kullback-Leibler super-efficiency under sparsity and robust shrinkage rules for large observations. We propose an efficient sampling algorithm for posterior inference. The performance of the proposed method is illustrated through simulation and two real data examples, the average length of hospital stay for COVID-19 in South Korea and adaptive variance estimation of gene expression data.

Variable selection methods with nonlocal priors have been widely studied in linear regression models, and their theoretical and empirical performances have been reported. However, the crucial model selection properties for hierarchical nonlocal priors in high-dimensional generalized linear regression have rarely been investigated. In this paper, we consider a hierarchical nonlocal prior for high-dimensional logistic regression models and investigate theoretical properties of the posterior distribution. Specifically, a product moment (pMOM) nonlocal prior is imposed over the regression coefficients with an Inverse-Gamma prior on the tuning parameter. Under standard regularity assumptions, we establish strong model selection consistency in a high-dimensional setting, where the number of covariates is allowed to increase at a sub-exponential rate with the sample size. We implement the Laplace approximation for computing the posterior probabilities, and a modified shotgun stochastic search procedure is suggested for efficiently exploring the model space. We demonstrate the validity of the proposed method through simulation studies and an RNA-sequencing dataset for stratifying disease risk.

We propose a novel family of self-decomposable Lévy processes where one can control separately the tail behavior and the jump activity of the process, via two different parameters. Crucially, we show that one can sample exactly increments of this process, at any time scale; this allows the implementation of likelihood-free Markov chain Monte Carlo algorithms for (asymptotically) exact posterior inference. We use this novel process in Lévy-based stochastic volatility models to predict the returns of stock market data, and show that the proposed class of models leads to superior predictive performances compared to classical alternatives.

Reference prior algorithms are primarily available for models that have asymptotic posterior normality (i.e., regular case), barring for a specific class of models whose posteriors are not asymptotically normal (i.e., non-regular case). In particular, the current reference prior methodology is contingent on models belonging to regular or non-regular cases. This highlights that the existing reference prior theory lacks a unified approach. A partial breakthrough in unifying the reference prior theory came with Berger et al. (2009) deriving an explicit form of reference prior for single group models (i.e., models with a scalar parameter or models that have all the parameters on equal footing or importance). Unfortunately, their approach does not generalize to multi-group models (i.e., models that have parameters’ subsets ordered according to their importance). In this paper, we show that their main result can be extended with modifications to multi-group models. As a consequence, we obtain a general scheme for deriving conditional reference priors. We also prove that the invariance property of reference priors under particular transformations hold for both regular and non-regular cases. We show the usefulness of our approach by computing reference priors for models that have no known reference priors.

Factor analysis is a popular method for modeling dependence in multivariate data. However, determining the number of factors and obtaining a sparse orientation of the loadings are still major challenges. In this paper, we propose a decision-theoretic approach that brings to light the relationship between model fit, factor dimension, and sparse loadings. This relation is done through a summary of the information contained in the multivariate posterior. A two-step strategy is used in our method. First, given the posterior samples from the Bayesian factor analysis model, a series of point estimates with a decreasing number of factors and different levels of sparsity are recovered by minimizing an expected penalized loss function. Second, the degradation in model fit between the posterior of the full model and the recovered estimates is displayed in a summary. In this step, a criterion is proposed for selecting the factor model with the best trade-off between fit, sparseness, and factor dimension. The findings are illustrated through a simulation study and an application to personality data. We used different prior choices to show the flexibility of the proposed method.

Three critical issues for causal inference that often occur in modern, complicated experiments are interference, treatment nonadherence, and missing outcomes. A great deal of research efforts has been dedicated to developing causal inferential methodologies that address these issues separately. However, methodologies that can address these issues simultaneously are lacking. We propose a Bayesian causal inference methodology to address this gap. Our methodology extends existing causal frameworks and methods, specifically, two-staged randomized experiments and the principal stratification framework. In contrast to existing methods that invoke strong structural assumptions to identify principal causal effects, our Bayesian approach uses flexible distributional models that can accommodate the complexities of interference and missing outcomes, and that ensure that principal causal effects are weakly identifiable. We illustrate our methodology via simulation studies and a re-analysis of real-life data from an evaluation of India’s National Health Insurance Program. Our methodology enables us to identify new active causal effects that were not identified in past analyses. Ultimately, our simulation studies and case study demonstrate how our methodology can yield more informative analyses in modern experiments with interference, treatment nonadherence, missing outcomes, and complicated outcome generation mechanisms.

In this article, we propose a novel spatial global-local spike-and-slab selection prior for image-on-scalar regression. We consider a Bayesian hierarchical Gaussian process model for image smoothing, that uses a flexible Inverse-Wishart process prior to handle within-image dependency, and propose a general global-local spatial selection prior that broadly relates to a rich class of well-studied selection priors. Unlike existing constructions, we achieve simultaneous global (i.e., at covariate-level) and local (i.e., at pixel/voxel-level) selection by introducing participation rate parameters that measure the probability for the individual covariates to affect the observed images. This along with a hard-thresholding strategy leads to dependency between selections at the two levels, introduces extra sparsity at the local level, and allows the global selection to be informed by the local selection, all in a model-based manner. We design an efficient Gibbs sampler that allows inference for large image data. We show on simulated data that parameters are interpretable and lead to efficient selection. Finally, we demonstrate performance of the proposed model by using data from the Autism Brain Imaging Data Exchange (ABIDE) study (Di Martino et al., 2014).

A simple and efficient adaptive Markov Chain Monte Carlo (MCMC) method, called the Metropolized Adaptive Subspace (MAdaSub) algorithm, is proposed for sampling from high-dimensional posterior model distributions in Bayesian variable selection. The MAdaSub algorithm is based on an independent Metropolis-Hastings sampler, where the individual proposal probabilities of the explanatory variables are updated after each iteration using a form of Bayesian adaptive learning, in a way that they finally converge to the respective covariates’ posterior inclusion probabilities. We prove the ergodicity of the algorithm and present a parallel version of MAdaSub with an adaptation scheme for the proposal probabilities based on the combination of information from multiple chains. The effectiveness of the algorithm is demonstrated via various simulated and real data examples, including a high-dimensional problem with more than 20,000 covariates.

Since the beginning of Bayesian nonparametrics in the early 1970s, there has been a wide interest in constructing models for binary response data. Such data arise naturally in problems dealing with bioassay, current status data and sensitivity testing, and are equivalent to left and right censored observations if the inputs are one-dimensional. For models based on the Dirichlet process, inference is possible via Markov chain Monte Carlo (MCMC) simulations. However, there exist multiple processes based on different principles, for which such MCMC-based methods fail. Examples include logistic Gaussian processes and quantile pyramids. These require MCMC for posterior inference given exact observations, and thus become intractable when the data comprise both left and right censored observations. Here we present a new importance sampling algorithm for nonparametric models given exchangeable binary response data. It can be applied to any model from which samples can be generated, or even only approximately generated. The main idea behind the algorithm is to exploit the symmetries introduced by exchangeability. Calculating the importance weights turns out to be equivalent to evaluating the permanent of a certain class of $(0,1)$-matrix, which we prove can be done in polynomial time by deriving an explicit algorithm.

Multiplex networks have become increasingly more prevalent in many fields, and have emerged as a powerful tool for modeling the complexity of real networks. There is a critical need for developing inference models for multiplex networks that can take into account potential dependencies across different layers, particularly when the aim is community detection. We add to a limited literature by proposing a novel and efficient Bayesian model for community detection in multiplex networks. A key feature of our approach is the ability to model varying communities at different network layers. In contrast, many existing models assume the same communities for all layers. Moreover, our model automatically picks up the necessary number of communities at each layer (as validated by real data examples). This is appealing, since deciding the number of communities is a challenging aspect of community detection, and especially so in the multiplex setting, if one allows the communities to change across layers. Borrowing ideas from hierarchical Bayesian modeling, we use a hierarchical Dirichlet prior to model community labels across layers, allowing dependency in their structure. Given the community labels, a stochastic block model (SBM) is assumed for each layer. We develop an efficient slice sampler for sampling the posterior distribution of the community labels as well as the link probabilities between communities. In doing so, we address some unique challenges posed by coupling the complex likelihood of SBM with the hierarchical nature of the prior on the labels. An extensive empirical validation is performed on simulated and real data, demonstrating the superior performance of the model over single-layer alternatives, as well as the ability to uncover interesting structures in real networks.